<h1>Groovy NGS Utils</h1>

<p>A set of Groovy and scripting support for working with Next Generation Sequencing data.<p>

<p>
   Groovy NGS Utils is designed to support easy creation of small to medium size 
   scripts that work with modern high throughput sequencing data, while still 
   maintaining high levels of performance.
</p>
<p>There are classes supporting a wide range of functionality including:
<ul>
    <li>Parsing VCF files and working with the variants inside them, including annotations
    <li>Parsing SAM and BAM files and working with reads
    <li>Parsing BED files and other formats representable as genomic intervals,
        and performing operations on these intervals
    <li>Working with FASTA, FASTQ and related formats
    <li>Many other miscellaneous functions!
</ul>

<p>Apart from providing all these individual classes, an important aspect is that
   all of these classes and interfaces interoperate. For example, a <code>Variant</code>
   implements the <code>IRegion</code> interface, and thus can be used with most of the
   APIs related to genomic intervals, etc</p>
